Variant report

Variant	rs6559711
Chromosome Location	chr9:85813844-85813845
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:85813794..85816602-chr9:85833659..85835490,2	MCF-7	breast:
2	chr9:85722110..85725029-chr9:85812448..85815231,2	MCF-7	breast:
3	chr9:85800689..85803340-chr9:85812087..85815667,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229109	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10114830	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10780577	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11139957	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1323767	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1323768	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1535747	0.86[JPT][hapmap]
rs1830771	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1924239	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2209191	0.84[JPT][hapmap]
rs4877742	0.86[JPT][hapmap]
rs4877746	0.86[JPT][hapmap]
rs4877750	0.86[JPT][hapmap]
rs744959	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs748415	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7848473	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7851233	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7851447	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7851474	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7855633	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7866798	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7871379	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893511	chr9:85495968-85833127	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv831642	chr9:85679425-85817338	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6559711	RMI1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85812600-85815000	Enhancers	Fetal Stomach	stomach
2	chr9:85813400-85814400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:85813400-85814600	Enhancers	Fetal Brain Male	brain
4	chr9:85813600-85814200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr9:85813600-85814400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:85813600-85815800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr9:85813800-85814000	Flanking Active TSS	Fetal Brain Female	brain
8	chr9:85813800-85814800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr9:85813800-85816000	Weak transcription	Brain Germinal Matrix	brain

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